/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 *
 * Written (W) 1999-2009 Soeren Sonnenburg
 * Written (W) 1999-2008 Gunnar Raetsch
 * Copyright (C) 1999-2009 Fraunhofer Institute FIRST and Max-Planck-Society
 */

#ifndef _SPECTRUMMISMATCHRBFKERNEL_H___
#define _SPECTRUMMISMATCHRBFKERNEL_H___

#include <shogun/lib/common.h>
#include <shogun/lib/Trie.h>
#include <shogun/kernel/StringKernel.h>
#include <shogun/features/StringFeatures.h>


#include <shogun/lib/Array.h>
#include <shogun/lib/Array2.h>
#include <string>

namespace shogun
{

#ifndef DOXYGEN_SHOULD_SKIP_THIS
/** joint list struct */
struct joint_list_struct
{
	/** ex index */
	unsigned int ex_index;
	/** index */
	unsigned int index;
	/** mismatch */
	unsigned int mismatch;
};
#endif

/** @brief spectrum mismatch rbf kernel */
class CSpectrumMismatchRBFKernel: public CStringKernel<char>
{
	public:
		/** default constructor  */
		CSpectrumMismatchRBFKernel();

		/** constructor
		 *
		 * @param size
		 * @param AA_matrix_
		 * @param nr_
		 * @param nc_
		 * @param degree
		 * @param max_mismatch
		 * @param width
		 */
		CSpectrumMismatchRBFKernel(int32_t size, float64_t* AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width);

		/** constructor
		 *
		 * @param l features of left-hand side
		 * @param r features of right-hand side
		 * @param size
		 * @param AA_matrix_
		 * @param nr_
		 * @param nc_
		 * @param degree
		 * @param max_mismatch
		 * @param width
		 */
		CSpectrumMismatchRBFKernel(
                                   CStringFeatures<char>* l, CStringFeatures<char>* r, 
		                   int32_t size, float64_t* AA_matrix_, int32_t nr_, 
		                   int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width);

		/** destructor */
		virtual ~CSpectrumMismatchRBFKernel();

		/** initialize kernel
		 *
		 * @param l features of left-hand side
		 * @param r features of right-hand side
		 * @return if initializing was successful
		 */
		virtual bool init(CFeatures* l, CFeatures* r);

		/** clean up kernel */
		virtual void cleanup();

		/** return what type of kernel we are
		 *
		 * @return kernel type 
		 */
		virtual EKernelType get_kernel_type() { return K_SPECTRUMMISMATCHRBF; }

		/** return the kernel's name
		 *
		 * @return name 
		 */
		virtual const char* get_name() const { return "SpectrumMismatchRBFKernel"; }

		/** set maximum mismatch
		 *
		 * @param max new maximum mismatch
		 * @return if setting was successful
		 */
		bool set_max_mismatch(int32_t max);

		/** get maximum mismatch
		 *
		 * @return maximum mismatch
		 */
		inline int32_t get_max_mismatch() const { return max_mismatch; }

		/** set degree
		 *
		 * @param deg new degree
		 * @return if setting was successful
		 */
		inline bool set_degree(int32_t deg) { degree=deg; return true; }

		/** get degree
		 *
		 * @return degree
		 */
		inline int32_t get_degree() const { return degree; }

		/** set AA matrix
		 * @param AA_matrix_
		 * @param nr
		 * @param nc
		 * @return true if set
		 */
		bool set_AA_matrix(float64_t* AA_matrix_=NULL, int32_t nr=128, int32_t nc=128);

	protected:

		/** AA helper 
		 * @param path
		 * @param joint_seq
		 * @param index
		 * @return AA helper
		 */
		float64_t AA_helper(std::string &path, const char* joint_seq, unsigned int index);

		/** compute helper
		 * @param joint_seq
		 * @param joint_index
		 * @param joint_mismatch
		 * @param path
		 * @param d
		 * @param alen
		 * @return helper
		 */
		float64_t compute_helper(const char* joint_seq, 
								 std::vector<unsigned int> joint_index, std::vector<unsigned int> joint_mismatch, 
								 std::string path, unsigned int d, 
								 const int & alen) ;

		/** compute helper all
		 * @param joint_seq
		 * @param joint_list
		 * @param path
		 * @param d
		 * @return helper
		 */
		void compute_helper_all(const char* joint_seq, 
								std::vector<struct joint_list_struct> & joint_list,
								std::string path, unsigned int d);

		/** computer all */
		void compute_all();

		/** compute kernel function for features a and b
		 * idx_{a,b} denote the index of the feature vectors
		 * in the corresponding feature object
		 *
		 * @param idx_a index a
		 * @param idx_b index b
		 * @return computed kernel function at indices a,b
		 */
		float64_t compute(int32_t idx_a, int32_t idx_b);

		/** remove lhs from kernel */
		virtual void remove_lhs();
		/** register the parameters
		 */
		virtual void register_params();
		/** register the alphabet
		 */
		void register_alphabet();


	protected:
		/** alphabet of features */
		CAlphabet* alphabet;
		/** degree */
		int32_t degree;
		/** maximum mismatch */
		int32_t max_mismatch;
		/**  128x128 scalar product matrix */
		float64_t* AA_matrix;
		/** length of the AA_matrix -- for registration */
		int32_t AA_matrix_length;
		/** width of Gaussian*/
		float64_t width;

		/** if kernel is initialized */
		bool initialized;

		/** kernel matrix */
		CArray2<float64_t> kernel_matrix ;
		/** kernel matrix length */
		int32_t kernel_matrix_length;
		/** target letter 0 */
		int32_t target_letter_0;
	
	private:
		void init();
};

}

#endif /* _SPECTRUMMISMATCHRBFKERNEL_H__ */
